Dear AFNI experts,
I used align_epi_anat.py to align anat and epi files before running the proc py using the below script.
align_epi_anat.py \
-epi2anat \
-anat "$subj"."$cond"_SurfVol.nii \
-epi epi."$subj"."$cond".slicemocoxy_afni.slomoco+orig \
-epi_base 0 \
-anat_has_skull yes \
-epi_strip 3dAutomask \
-giant_move \
-volreg off \
-overwrite
Pre-alignment (upper image) was not bad but I wanted to make it better so ran the script, but I found that epi image became completely off from anat after running the align_epi_anat (below image). Could you please let me know how can I fix this?
Best,
JW
